Variant report

Variant	nsv519184
Chromosome Location	chr2:56154316-56163904
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:56156617-56157099	A549	lung:	n/a	chr2:56156796-56156809 chr2:56156796-56156809
2	CEBPB	chr2:56156700-56156963	HepG2	liver:	n/a	chr2:56156796-56156809 chr2:56156796-56156809
3	CEBPB	chr2:56154142-56154492	IMR90	lung:	n/a	chr2:56154322-56154333
4	CEBPB	chr2:56154149-56154501	Hela-S3	cervix:	n/a	chr2:56154322-56154333
5	CEBPB	chr2:56154185-56154462	K562	blood:	n/a	chr2:56154322-56154333
6	CEBPB	chr2:56156684-56156955	K562	blood:	n/a	chr2:56156796-56156809 chr2:56156796-56156809
7	CEBPB	chr2:56154143-56154495	A549	lung:	n/a	chr2:56154322-56154333
8	CEBPB	chr2:56156644-56156995	IMR90	lung:	n/a	chr2:56156796-56156809 chr2:56156796-56156809
9	CEBPB	chr2:56154142-56154498	HepG2	liver:	n/a	chr2:56154322-56154333
10	CEBPB	chr2:56154199-56154469	H1-hESC	embryonic stem cell:	n/a	chr2:56154322-56154333
11	CEBPB	chr2:56154099-56154490	MCF-7	breast:	n/a	chr2:56154322-56154333
12	CTCF	chr2:56155400-56155550	A549	lung:	n/a	n/a
13	CTCF	chr2:56162420-56162570	SAEC	small airway:	n/a	n/a
14	CTCF	chr2:56155346-56155483	K562	blood:	n/a	n/a
15	CTCF	chr2:56155400-56155429	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr2:56155384-56155449	MCF-7	breast:	n/a	n/a
17	CTCF	chr2:56155285-56155474	K562	blood:	n/a	n/a
18	CTCF	chr2:56155420-56155570	MCF-7	breast:	n/a	n/a
19	CTCF	chr2:56155344-56155417	MCF-7	breast:	n/a	n/a
20	CTCF	chr2:56158640-56158790	HCM	heart:	n/a	n/a
21	FOS	chr2:56163568-56163815	MCF10A-Er-Src	breast:	n/a	chr2:56163673-56163681 chr2:56163673-56163681 chr2:56163674-56163681
22	FOS	chr2:56163643-56163845	MCF10A-Er-Src	breast:	n/a	chr2:56163673-56163681 chr2:56163673-56163681 chr2:56163674-56163681
23	FOS	chr2:56163518-56163819	MCF10A-Er-Src	breast:	n/a	chr2:56163673-56163681 chr2:56163673-56163681 chr2:56163674-56163681
24	FOS	chr2:56163602-56163858	HUVEC	blood vessel:	n/a	chr2:56163673-56163681 chr2:56163673-56163681 chr2:56163674-56163681
25	FOXA1	chr2:56154245-56154487	T-47D	breast:	n/a	n/a
26	GATA3	chr2:56163448-56163974	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr2:56158316-56158780	MCF-7	breast:	n/a	n/a
28	GATA3	chr2:56163351-56163978	SK-N-SH	brain:	n/a	n/a
29	GATA3	chr2:56158499-56159008	MCF-7	breast:	n/a	n/a
30	GATA3	chr2:56158405-56158798	MCF-7	breast:	n/a	n/a
31	GATA3	chr2:56158398-56158733	T-47D	breast:	n/a	n/a
32	IRF1	chr2:56156551-56156658	K562	blood:	n/a	n/a
33	KAP1	chr2:56154259-56154640	U2OS	brain:	n/a	n/a
34	MAZ	chr2:56160389-56160402	GM12878	blood:	n/a	n/a
35	MXI1	chr2:56161771-56161812	GM12878	blood:	n/a	n/a
36	PBX3	chr2:56163422-56163951	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr2:56163519-56163697	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr2:56158528-56158585	Gliobla	brain:	n/a	n/a
39	RELA	chr2:56159940-56160383	GM12891	blood:	n/a	n/a
40	RFX5	chr2:56154845-56154904	K562	blood:	n/a	n/a
41	SETDB1	chr2:56154269-56154762	U2OS	brain:	n/a	n/a
42	SIN3AK20	chr2:56158254-56158918	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr2:56158556-56158758	MCF-7	breast:	n/a	n/a
44	ZNF217	chr2:56158406-56158785	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:56159616..56161838-chr2:56172027..56174900,2	MCF-7	breast:
2	chr2:56158828..56161506-chr2:56178207..56181197,2	MCF-7	breast:
3	chr2:56149060..56151450-chr2:56151647..56155915,3	MCF-7	breast:
4	chr2:56152117..56154083-chr2:56155709..56157314,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC85A-4	chr2:56163008-56163084	ucscGeneNc_uc002rzk_2
2	lnc-EFEMP1-4	chr2:56158056-56158694	NONHSAT070809
3	lnc-EFEMP1-4	chr2:56155293-56158694	ucscGeneNc_uc002rzl_1

Variant related genes	Relation type
EFEMP1	TF binding region
ENSG00000202344	chromatin interactions
ENSG00000272180	chromatin interactions
ENSG00000115380	chromatin interactions

Extended variants
information (count: 280 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:280 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10469935	chr2:56154316-56154317	Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs574059245	chr2:56154411-56154412	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs542245110	chr2:56154415-56154416	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs139969018	chr2:56154441-56154442	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs183990707	chr2:56154513-56154514	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs561829884	chr2:56154529-56154530	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs546090020	chr2:56154600-56154601	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs188313061	chr2:56154717-56154718	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs191283051	chr2:56154724-56154725	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs547878687	chr2:56154755-56154756	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs567796521	chr2:56154758-56154759	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs184987244	chr2:56154770-56154771	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs369453526	chr2:56154771-56154772	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs371369048	chr2:56154810-56154811	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs190295747	chr2:56154872-56154873	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs141797128	chr2:56154894-56154895	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs144523895	chr2:56154913-56154914	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs148536853	chr2:56154918-56154919	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs376241520	chr2:56154941-56154942	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs201220756	chr2:56154957-56154958	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs75168075	chr2:56154974-56154975	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs567552041	chr2:56155041-56155042	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs377128599	chr2:56155046-56155047	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs114629833	chr2:56155053-56155054	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs574242705	chr2:56155059-56155060	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs544256571	chr2:56155085-56155086	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs35638669	chr2:56155086-56155087	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs548823613	chr2:56155120-56155121	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs6707184	chr2:56155140-56155141	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs556646923	chr2:56155151-56155152	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs151042429	chr2:56155212-56155213	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs545751646	chr2:56155213-56155214	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs545568307	chr2:56155253-56155254	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs559633049	chr2:56155261-56155262	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs559616418	chr2:56155264-56155265	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs528280684	chr2:56155309-56155310	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs542072843	chr2:56155318-56155319	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
38	rs140743284	chr2:56155339-56155340	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs530257919	chr2:56155340-56155341	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs550307432	chr2:56155356-56155357	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs144603191	chr2:56155370-56155371	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
42	rs532557718	chr2:56155385-56155386	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs548189886	chr2:56155398-56155399	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs371425948	chr2:56155430-56155431	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs182119388	chr2:56155469-56155470	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs76634416	chr2:56155509-56155510	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs113959191	chr2:56155528-56155529	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs568328410	chr2:56155571-56155572	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs536704283	chr2:56155598-56155599	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs557041186	chr2:56155678-56155679	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56153400-56154400	Enhancers	A549	lung
2	chr2:56156200-56157400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:56156600-56157000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:56160000-56160200	Enhancers	GM12878-XiMat	blood
5	chr2:56161400-56162200	Enhancers	Dnd41	blood
6	chr2:56161600-56161800	Enhancers	GM12878-XiMat	blood
7	chr2:56163800-56164000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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